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Tuesday, January 22, 2013

One of themes of
this book is that if we are to satisfy our curiosity about the
universe around and within us, we will need to use our imaginations
to the best of our abilities, because the universe as we perceive
with our physical senses will only take us so far. We saw this first
in chapter two, in which our robotic exploration of the solar system
revealed worlds which we had not foreseen, at least partly because we
had not completely unleashed our imaginations on the possibilities.
In chapters three and four we were forced to use our imaginations
again to picture how the world of the ultra-tiny, or atoms and
electrons, works, by suspending our common-sense ideas and
perceptions so that such things could become real and not mere
philosophical concepts, tangible things we could get our minds around
and acquire a sense of their true nature. My point is that in these
journeys we have gained a certain intellectual satisfaction – real
questions leading to real answers – but again we are being warned
that clinging to the world as modeled by our eyes and visual cortexes
is a habit we are going to have to resist, one way or the other, if
we expect to keep making progress.

This chapter is on
biology, which is why I begin with this emphasis on imagination, for
with the possible exception of quantum mechanics, I believe nowhere
is imagination more required than on the subject of life. Living
things, their origins, their myriad shapes and actions combined with
their underlying foundations, and how their marvelous,
interdependent, and beautiful adaptivity to all environments they
find themselves in, is a series of mysteries that will not yield to
the unimaginative mind, however much plodding thought is brought to
bear on them. Unconvinced? Then let’s start with the big
question, the question even the most renown scientists have been
beating their heads against right up to today: What is life? We see
it practically everywhere we look (at least on this isolated, tiny
planet) and we generally find we have no difficulty in distinguishing
it from the world of the non-living.

I think at this
point most of us would stop and agree, perhaps after some careful
thought, that there is something essential about living things. The
impression of this essentialness, this intentionality
I will call it, is indeed overwhelming, and easily hits us on the
head as the prime divider between life and everything else. All
non-living things seem to follow the laws of physics in a dumb,
obvious way: a pebble thrown into the air traces out a perfect
mathematical parabola as it interacts with the law of gravity,
finally striking earth in a completely predictable place at a
completely predictable time, given that we know its initial speed and
angle with respect to the ground. A pebble thrown into the air …
but what about a butterfly? When we watch a butterfly we put away
our calculators and measuring instruments, and simply watch in
wonder. A butterfly doesn’t blindly follow a parabola, it –
well, it seems to do whatever it decides to do, which is why making
measurements and calculations are pointless. A butterfly flies away,
perhaps never to be seen again. Or maybe it alights on a flower and
gazes at us, seemingly as equally puzzled by us as we are of it. We
are just certain there’s something going on behind those tiny eyes.
Something inexplicable. Something essential. Something that gets
down to what makes a pebble just a pebble but a butterfly something
... at the risk of being misunderstood, miraculous.

We still have taken
only a few steps in our attempt to define life, however. For the
next question is, is our butterfly, and by implication ourselves,
truly miraculous?

* * *

Let us try a
different tack. Richard Dawkins, in The
Blind Watchmaker, proposes
a definition of biology that is unusual but which he claims to be
perfectly workable: biology is the study of complex things that
appear to have been designed for a purpose. I speak of
intentionality, but complexity plus the appearance of design provides
us with another way of describing it, perhaps an even better way to
make progress. Dawkin’s point when applied to our butterfly is
threefold; first, like all life forms it is far, far more complex
than the pebble, far more complex than our solar system even; second,
not only does it act as though it has a mind capable of intentions
and a body capable of carrying those intentions out, it gives all the
appearance in the world to have been designed that way, designed to
fly (as well as many other things); and third, and most
significantly, there is an intimate relationship between complexity,
intentionality, and design. Flying is not a simple thing, not the
way butterflies do it at any rate, so complexity plus design, or as I
call it, intentionality, appears to improve our handle on what we
mean when we say something is alive.

But is it enough?
Or for that matter, is it really true? Living things do not always
appear to be complicated. Anyone dissecting a butterfly – no easy
task, admittedly – would marvel at its many interlocking intricate
parts, but what about the simple amoeba? Or a bacterium? At first
sight, such things do not appear to be particularly complex, but we
all agree that they are alive; that, like the butterfly, they appear
to move under the guidance of some internal intentions, some essence
which non-living things, even complex ones like computers, do not
possess.

Most of us, I
suspect, will find ourselves easily moving along some kind of
reasoning like this, perhaps without thinking about it very much. It
does seem to handle our common sense objection to calling complex
things like computers and airplanes biological while keeping “simple”
things like bacteria and amoebas in the same camp as butterflies and
human beings. Living things, from the simplest up to the most
complex, really do seem to have some special quality or essence that
ordinary matter lacks, whatever else that matter has. We almost can
feel it there, at the most basic levels, and we are certain that we
would never have any difficulty in distinguishing a living thing from
the non-living, based on that feeling. Wherever in the universe we
might find ourselves, the question of whether we were amongst life or
not would appear to be elementary.

* * *

Or would it? To our
astonishment, our common sense view of things biological begins to
disintegrate the moment we apply curiosity and imagination to it, to
dissect it and look into it at the finest levels science allows us to
probe. In doing so, try as we might, we never encounter this special
essence or quality which seems so obvious at first sight. Instead,
what we do find, when we break out our detectors and other scientific
instruments, is that living things are composed of atoms and
moledcules like everything else, albeit not in the same elemental
proportions, yet acting according to the same laws of physics and
chemistry as everything else. The mechanical, Newtonian universe of
objects and forces, modified by quantum effects on the smallest
scales, appear all that is needed to explain why butterflies fly, or
mate, or find food, or stare at us with the seeming same curiosity
that we feel gazing upon it. All our initial impressions, and all
the stories that have been told and retold aside, there appears no
miraculous special something that we can affix to or inject matter
with to make it come alive; no energy fields, no forces, no
protoplasm, no elixir of the living, nothing we can pump into Dr.
Frankenstein’s reassembled parts of corpses which will make it
groan and open its eyes and have thoughts and feelings and break its
bonds to move in accordance with them. There is nothing like that
whatsoever. No, whatever it is that characterizes life lies
elsewhere.

But the impression
of such a force is so strong, so deep, so instinctual that, try as we
might, we cannot simply abandon it without at least wondering why it
is there, where it comes from, and what it tells us. Something
is there, of that there can be no question.

Intentionality.
Complexity. Design. Try to put aside your ordinary impressions and
perceptions of things, and seed your mind, germinate in your mind,
take root and push out of the soil and put forth leaves and vines in
your mind, the theme that to satisfy our curiosity we must look at
the world from a different perspective, the one that imagination
unlocks. Very often, we find that when we look closely, what we
thought we were seeing fades away, yet is replaced by something just
as amazing – no, more so.

Let us start with
the simplest of things that could be called living. Consider the
virus. Here is something both considerably smaller and simpler than
the smallest, simplest bacterium, all biologists would agree. But on
the most microscopic of scales, that of individual atoms and
molecules, even the simplest virus turns out to be a machine of
remarkable complexity. At the very least it has to be able to
recognize a host cell it can parasitize, whether it is a cell in your
body or a bacterium (in which case it is called a bactaeriaphage),
somehow figure out the molecular locks and other gizmos which cells
use to protect themselves from invasion, penetrate the defenses, then
usurp the molecular machinery the cell uses to replicate itself,
perverting the cell into a factory for producing many more copies of
the virus, copies which then have to figure out how to break out of
the cell in order to repeat the cycle on other cells or bacteria, all
the while avoiding or distracting the many other layers of defenses
cells and bodies use to protect themselves from such invasions.

Biologists still
debate whether viruses can be legitimately counted among the various
kingdoms and domains of life, but there is no doubt that their hosts,
whether bacteria or other single celled organisms or multicellular
organisms, can be classified in the great Tree of Life, from which
all other living things, be they plants, animals, fungi, or you,
diverge from. And what dominates this tree, right down to the most
primitive beginnings we have yet been able to detect, is a level of
complexity that we simply do not encounter among the great many more
things than don’t belong on this tree, from rocks to stars to solar
systems to galaxies.

So after all this,
have we cornered our quarry? We started with the at first sight idea
that life possessed some special quality or substance or essence,
then realized that we could not find that essence however hard we
looked. But what we did find was that living things, even the
simplest of them, showed a level of complex organization well beyond
the most complex of non-living things.

Life is
special. I don’t want to lose sight of that. We are fully
justified in our grand division of matter into the non-living –
things we explain only by the laws of physics and chemistry at a
simple level – and the living, all the things we must also apply
whatever biology has to teach us. What I have been trying to show is
that, whatever that specialness is, it isn’t as obvious as it
appears upon first sight. It is more subtle, involving a number of
characters and qualities, one of which is complexity and another the
appearance of design or purpose.

* * *

Again, I say that
life truly is special. It is early May, and I have just come home
from a walk through Pennypack Park, one of the many lovely natural
places which skirt the city where I live, Philadelphia, one of
several cities along the eastern edge of North America. I would
love one day to walk on the moon or on the red soil of the planet
Mars, but what I have just experienced would be utterly lacking in
those dead, albeit fascinating places. In the spring in this part of
the world, as in many other parts of our planet, every sense is
roused to life by the call of the wild. Not only are you surrounded
by the verdant green of new buds and flowers and grasses, but also by
a cacophony of whistles, chirps, tweets, and other rhythmic sounds
which reminds you that you that new life is all about, some of it
still rustling itself to full wakefulness after winter but much of it
already in the air and alit on the many twigs and branches. And even
without vision and sound, you can still smell the musty beginnings of
stirrings things, the scents of enticing blossoms and irritating
pollens, and you can still feel the grass between your toes and the
softness of young leaves on your skin as you brush by the
undergrowth.

Here I have spoken
of complexity and the appearance of purpose and meaning, and perhaps
that is exactly what our scientific mission into the heart and soul
of biology requires, but this is one place where, I have to submit,
we will never really capture the essence of what we are studying.
Life is something that has to be experienced, and only living things
themselves have the capacity, as far as we know, to experience
anything. So, in a sense, our quest to satisfy our curiosity begins
with the admission that, at least for the world of the living, we
never can completely satisfy it.

Am I going to give
up, then? No, because, as I have maintained up to this point,
curiosity combined with imagination and the scientific method can
undo any knot, unlock any riddle, however baffling and impervious it
may seem. I have even suggested a starting place even, this idea of
complexity combined with apparent purposefulness, an idea I hope to
build upon and demonstrate just how powerful it is. I think we can
agree that it is a good starting place. Biological things, even the
simplest of them, are highly complex, we now see, and there does seem
to be something to this notion of being imbued with purpose, however
that comes about. If we can make some progress on this front, then
perhaps in the end we will satisfy our intellects after all, as
impossible as that seems looking at things from their beginnings.

* * *

Actually, I would
like to strike out first on a different front than is typical in
tomes on biology. I would like to retreat back to simple matter, of
the kind we started to explore in chapter four, and work up to what I
see as an essential question: can the laws of physics and chemistry,
as we have come to know them, even provide a platform for the vast
complexity of living things? In other words, do atoms, those basic
building blocks of all things material, even allow for the enormous
intricacies let alone purposefulness of the biological world?

This is a very good
question for it turns out, at least for the great majority of atoms
that we investigate toward this end, the answer is a clear and
resounding No.
Try as hard as we can, we find that when we begin assembling most
atoms into more and more complicated molecules or other structures,
they aren’t very cooperative in this process. No, things fall
apart, often violently, even if we can figure out a way of putting
them together. For the great majority of the kinds of atoms to be
found in nature, constructing an edifice of complexity sufficient for
life is a hopeless task. They simply will not stay put and do as
they are told.

All that is with
one, yes really only one, fortuitous exception, and one that we began
to explore in the previous chapter. The carbon atom. Atomic number
six on our periodic chart, a chart which now runs to over a hundred
if we include the extremely short-lived ones humans have made in
laboratories, is truly special. Carbon is what makes it all
possible, to the point where we can confidently say that if that if
this one lone atom out of the dozens had proved impossible for the
universe to produce in any significant quantities, neither you nor I
nor any of the myriad millions of species of life we share this
planet – on perhaps any planet – with would have any chance at
existing. Carbon alone is not sufficient for life, but it is
absolutely necessary. Of all the other elements in the biological
stew, perhaps substitutes could have been found, but no element,
under any conditions imaginable, appears a likely alternative to
carbon. This is because no other element yet discovered or made
could take its place as the backbone of the sizes and varieties of
the molecular components needed to make life, even the simplest forms
of life, possible. I will even go as far to say that if an
alternative form of life is ever found, if carbon isn’t at its
roots than neither is chemistry.

Carbon, indeed, is
so important that it is the only element whose existence was
predicted by the fact that living things do exist. All of the
naturally occurring elements in the universe today come from one of
two sources: either they were made in the first few minutes of the
universe’s existence, in the Big Bang which we will come to in a
later chapter, or they were made in the cores of the many trillions
of massive stars that have come and gone since the beginning. The
reasons for both is the same: larger, more complex atomic nuclei –
the core of protons and neutrons which make up the center of atoms
and ultimately determine their respective element’s properties –
have to be made from the simpler ones, ultimately from the simplest
of them all: hydrogen, atomic number one, a single proton (sometimes
combined with one or even two neutrons). This is done by smashing
two smaller nuclei together to make the larger one, a process which
requires extremely high pressures and temperatures because all nuclei
are positively electrically charged and ordinarily repel each other
unless they can be brought close enough together to be captured by
something called the strong nuclear force. Such conditions existed
naturally only in the moments after the Big Bang and today in the
hearts of stars, particularly the larger, hotter stars. Essentially,
to create a carbon atomic nucleus of six protons and six neutrons,
what must happen is that three helium four nuclei, each consisting of
two protons and two neutrons apiece, must be welded together in
exceedingly short order, within a millionth of a millionth of a
second, and then held together until they can relax and become
stable. This so-called “triple-alpha” process (an alpha particle
is a helium four nucleus) would itself seem to be an insurmountable
barrier to carbon and all the elements beyond, but surprisingly that
turns out to be not so: the pressures and temperatures which come to
exist in large stars – stars large enough to explode or somehow
spew their core substances into intergalactic space, making all those
large atomic nuclei available to new generations of stars and planets
such as our own, not to mention our own existence – are sufficient
to guarantee this process will happen enough to account for all the
carbon we are going to need.

With one problem.
This problem lies in the fact that our newborn carbon nucleus is
ringing and pulsing with so much energy that it should almost
instantly fragment into smaller pieces. What we need is some kind of
stable “resonance” at such high energies, which will allow the
newly born nucleus to hang together just long enough to relax by a
variety of processes into a lower, energetically stable state. But
when the details of Big Bang and stellar nucleosynthesis were being
worked out in the 1940’s and 50’s, no such resonance state was
known, nor was there any theoretical reason – theoretical from the
standpoint of physics at that time that is – to think one should
exist.

The problem was
solved by the single and to this day to my knowledge lone instance of
the so-called Anthropic Principle being used to successfully explain
an actual physical fact. If you are not familiar with it, the
Anthropic Principle, in its most basic, common-sense form, is simply
the statement that since we exist in this universe, the laws
governing it must be compatible with our existence (this seems
obvious, but there are other versions of the Anthropic Principle
which are more controversial). In this case, what the principle
insists is straightforward and simple: it insists that since the
element carbon does exist in sufficient quantities for our existence,
there must be a resonance energy level available for the newly bred
nuclei. The Anthropic Principle is not an argument physicists are
usually enamored of, but one group was sufficiently impressed by the
line of reasoning to take an actual look and see if the resonance
level really did exist. Lo and behold, they found that it did. In
fact the discovery not only explained the existence of carbon in
sufficient quantities in the universe, but also of the many elements
that are in turn built up from it: oxygen, neon, silicon, indeed
basically the entire periodic zoo of elements we find, to varying
degrees of magnitude, present in the universe today.

* * *

So, carbon exists.
It isn’t a very common element, and the fraction of it that does
reside in our universe in conditions where life can form, is
relatively small. But it is enough to account for, not just you and
I, but all of the manifestations of biology all about us, almost
anywhere you go on this planet, and probably what other worlds or
places we may one day find life. The next question is, what is it
about carbon that gives it its uniqueness, its specialness, its
ability to construct the large and complex and seemingly purposeful
phenomena that we call living things? What does carbon have that no
other atom seems to possess, however hard we play with them and build
castles in the air from them? Why do these carbon-based organisms
which are found with such fecundity on Earth and hopefully on at
least some other planets or moons or asteroids or places we’ve yet
to think of, exist, continue to exist, and have existed for so long?
Yes, carbon is special, but special in what ways, so many ways that
no other atom has a prayer of filling its role?

The answer to this
question is answered by a combination of chemistry and physics, some
of which I have already explored in the last chapter. It involves
two separate characteristics of carbon, chemical as well as physical
characteristics, characteristics which carbon and carbon alone
possesses, characteristics which we can never even mock up in any
other element, however hard we try.

One of those
characteristics is smallness. It is not coincidence that the great
majority of the atoms which constitute life are to be found at the
top of the periodic table, where the smallest and simplest of atoms
resides. One reason for that no doubt is that small atoms are, due
to the processes which forge them, simply more common than large
ones. But another reason, the key reason, is that smallness means
that these atoms can come much closer to each other in the
bond-forming process, resulting in bonds that are much stronger and
stabler than larger atoms can form. It is, in fact, well accepted,
that the small sizes of the first and second rows of the periodic
table account for much of the uniqueness of their chemistry,
especially in the ways they differ from their heavier cousins, even
in the same column. To give an example, sulfur, selenium, and
tellurium are much more similar to each other than the first member
of their column, oxygen. This is a statement which could be made for
nitrogen and boron as well, and even, although to a lesser extent,
lithium and fluorine. Small atoms make for short, strong bonds,
something necessary if we are to build up to the size and complexity
of living things and have them remain stable. Even a structure as
small as a bacterium demands a level of complexity which only carbon
and other small atoms can provide.

So smallness is
important, but it is not sufficient. The reason for this can be
found by examining the other elements in the first row, for example
hydrogen, which can bond with one and only one other atom; usually
another hydrogen atom, making the molecule H2,
which is almost entirely what we are dealing with when working with
hydrogen on the scale of pressures and temperatures we are accustomed
to. Likewise, nitrogen and oxygen, also essential to life, appear to
form stable binary molecules, N2
and O2,
which do not spontaneously join together into longer, more
complicated structures but make up the most common constituents of
this planet’s air we breathe, which is about 78% N2
and 21% O2.

Following this line
of argument, shouldn’t stable C2
molecules exist also, thereby undermining this theme of small atoms
making large, structurally stable molecules, and once again pulling
the rug out from underneath our feet in our quest to make the large,
complex yet stable molecules and molecular edifices that biological
things demand? Here is the interesting part, however; the neat trick
by which nature refuses to be obvious but instead manages to provide
us with exactly what we were looking for. For it turns out that C2
does not (or only rarely) exist, indeed is not normally stable, and
once again we are allowed to proceed in the directions biology calls
upon us to follow.

O2
and N2
are stable due to the smallness of oxygen and nitrogen atoms, but
there are limits to how large you can build these small, compact
molecules. These limits are inherit in the kinds of bonds that atoms
can form with one another. In chapter four, I introduced the idea of
the molecular orbital as the bond between two atoms created by the
combination of the atoms’ atomic orbitals. The strength of the
resulting bond depends on how well the atomic orbitals can overlap in
space. This is where smallness comes into play. The bond between
two hydrogen atoms is very strong because these atoms are very small
and can approach each other quite closely, allowing for maximum
overlap.

A picture being
worth a thousand words, let me recapitulate some of the material for
the preceding chapter about molecular bonds. If you’ll remember
the case of the H2
molecule, we explained the bond as the overlap of s orbitals, in
which two new orbitals came into existence:

one bonding one
between the atoms, which strengthens the bond, and one antibonding
orbital, which weakens it:

The bonding MO in this case has a name: it is called a sigma,
or σ,
bond, as chemists call them. This sigma bond, to reemphasize, is
formed by the overlap of the s
orbitals in the two hydrogen atoms, but more broadly, sigma orbitals
/ bonds are at highest density between the two orbitals. There is
another type of σ
bond, however, which can be formed by the overlap of p
bonds. If you’ll recall, these bonds have the general shape

Here,
the lines drawn represent the y (vertical) and z (horizontal) axes,
while the x axis orbital would point at straight angles through the
page. This is why I say that there are three p
orbitals, all perpendicular to each other. Now, if you imagine the
pz
orbitals of two atoms, lying along the horizontal line above, the z
axis, you can see how they too can overlap to form sigma orbitals,
just as the s
orbitals did. Very nice, and exactly what happens for many elements
in the first row of the periodic chart. But now, remembering that
there are three p
type orbitals, you can see that in the case of two atoms the pz
and the py
don’t directly overlap, but appear to be parallel to each other.
Hang in here. For I think I can make this clear with a few more
diagrams and words. The orbital above, which I called py
because the lobes are oriented in the y direction along the axis,
cannot form σ
(sigma) molecular bonding orbitals, because they don’t directly
overlap between the atoms. But there are other kinds of bonds, bonds
in which the overlap of the atomic orbitals is not so direct and
obvious. The py
and pz
type orbitals possessed by the above atom are a perfect example of
this. Still, using our imaginations, we can see that, although these
orbitals do not combine headlong, there is nevertheless an overlap,
an oblique or sideways overlap, between the lobes of the orbitals,
for both the px
and pz
orbitals, if the atoms involved approach each other closely enough.
The overlap is not as strong as with the pz
orbitals, which directly overlap in the plane of the paper to form σ
bonds,
just like the s
orbitals do, but it is there nevertheless. It is strong enough that
we can construct new molecular orbitals, or bonding orbitals, using
these oblique or sideways oriented atomic orbitals. Chemists have a
name for these kinds of bonding orbitals as well; they are called π
orbitals or pi bonds, again applying our habit of using Greek
letters, in this case the letter π
which we call pi. An example of this sideways, pi type bond is given
below:

The
nucleus of each atom lying at the center of the two py
lobes is shown by the intersection of the x and z axes, while the py
orbitals are the areas “smeared out” above and around them. Can
you see that there can be sufficient overlap, and hence bond
formation, between the two atoms using their py
orbitals, shown by the grey regions, provided that they can be
brought close enough together? Also, is it clear to the eye that the
π
bonds are not as strong as sigma (or σ)
bonds, composed of either s
or px
orbitals, which occupy the space directly between the atomic nuclei,
and that to have any strength at all the respective atoms must be
able to approach each other very closely, which in turn means that
only small atoms form stable π
bonds? I think yes, just by looking at them, we can see that π
bonds will be weaker and easier to break than σ
bonds, a disparity that can only increase as we look at larger and
larger atoms.

So.
What has all this got to do with living things and their chemical
makeup? As it turns out, plenty. The molecules N2
and O2
are stable only because of the smallness of their atomic sizes, and
so can have as many as two (as in N2
or O2)
π
bonds, in addition to their σ
bonds – this, by the way, is why we call them triply-bonded or
doubly-bonded molecules.

Still,
they would prefer for energetic reasons to exchange these π
bonds and create or join in with molecules where all the bonding is
of σ
character; that is why we find how easily they combine with, for
example, hydrogen atoms to make the simple molecules of water (H2O)
and ammonia (NH3).
Even carbon, which we are reserving as the basis of many
manifestations of life, is often found bound up with hydrogen too, in
this case to yield the simple molecule of methane (CH4)
as seen in the last chapter. I should also mention to make this
clearer that this is the same reason why third level elements, even
those in the same family of nitrogen and oxygen – phosphorus and
sulfur – do not easily form π
bonds, as the larger size of these atoms do not allow them to
approach each other closely enough; thus, we do no see p2
or s2
molecules, but more complex structures (this is also because these
atoms have available 3d
orbitals for additional bond forming, but we will not go there).

As
we alluded to in chapter 4 carbon’s versatility comes forth even in
these most basic of molecules. Using sp3
(again, you may have to refer to the last chapter to refamiliarlize
yourself with them) hybrid orbitals, carbon can form as many as four
strong, sigma bonds with other atoms, a feat no other atom can boast
of. Since up to four of those atoms it can combine with is another
carbon, we can imagine a vast network of sigma-bonded carbon atoms, a
network that can grow virtually as large, and as complicated, as it
likes. Such networks in fact do exist, and as already mentioned we
call them diamonds, allegedly the hardest substance in the universe.
What is more important for this discussion is that if the simple atom
of carbon can yield the hardest of materials in the universe, then
the creation of living things would appear to be a natural outflow of
this process of bonding one carbon atom to another. Moreover, with
each carbon atom having four “hands” or valence electrons to
offer any other atoms it may encounter, we should be able to come up
with just about any large, complex, stable molecular structure we
can imagine.

Indeed
we can, and have, and the subject even has been given a special name:
organic chemistry. That’s right; carbon is so unique in its
abilities to build complex structures and edifices – meaning large,
complicated molecules – that it and it alone is awarded the very
special prestige of having an entire branch of chemistry constructed
around it. As a matter of fact, go to any university’s web site
and start checking out the chemistry courses and you will see that
the very subject appears to have two major branches: organic and all
the rest, some of the rest actually being called inorganic chemistry.
No other element even comes close to commanding such respect. So we
finally see carbon’s commanding role being due to its unique
ability to form the backbone of an almost infinite variety of
molecular sculptures. And it is exactly that kind of versatility we
are going to need if we are to make any sense of the fantastically
complex, seemingly purposeful assemblages of atoms and molecules
which comprise the roots and foundations of the vast panoply of
biology spread before us. When it comes to satisfying our
curiosities, that is one nail we can pound in completely and begin
our explorations around. We can now say that basic, straightforward
physics and chemistry do allow for biology, though, again this must
be stressed, they are nowhere close to explaining it by themselves.
The explanation requires something else, something that we have been
edging toward, a grand idea or set of ideas that provide the
gratification we have been seeking. It is time to fully enmesh
ourselves in these ideas, and bask in the glory of what we have been
seeking.

* * *

So,
the chemistry of carbon, along with a handful of other atoms like
oxygen, nitrogen, hydrogen, sulfur, phosphorus, and a smattering of
other trace elements gives us all the building blocks we need to
create human beings, elm trees, barnacles, tyrannosaurs, and
paramecia, but that doesn’t explain how or why the blocks manage to
come together in the right ways. Brachiosaurs, which were very
large, plant eating dinosaurs, may be built from the same carbon and
nitrogen and all the other atoms in our own biological grab-bag of
goodies, but no amount of blending, whipping, hurling around, or
piling one thing on top of another will never give us that Jurassic
eating machine, or anything else that could be even remotely
construed as alive in any sense of the word.

Here
we are in our quandary, because we know the answer provided by
thousands of years of folk-wisdom, occasionally dressed up in full
theological garb. God, or some pantheon of gods, or something
supernatural and miraculous, conjured up all the millions of species
that creep, run, swim, fly, fester, or patiently await for the
comings and goings of seasons and suns, so goes the wisdom of the
ancients. Most people who have ever lived, and probably most of
those alive at this moment, find this answer satisfactory. But if we
are to truly gratify our curiosity, we have to accept that this is no
answer at all. It is just another waving of the wand of the
miraculous, with results unexplained and unexplainable. Or to put it
another, yet more devastating, way: if God or some set of gods
explains the complexity plus appearance of purpose we find in
biology, then what explains Its / their equally perplexing purposeful
complexities? It’s an infinite regress, which leads nowhere and
satisfies nothing in the end. The only possible way this
“explanation” can work is if we can come up with something that
is intelligent, intentional, creative, and yet somehow simple. My
suspicion is that is exactly the kind of reasoning, at a largely
sub-conscious level, the theological inclined are actually all about.
To which all I can say is, I cannot dismiss it completely out of
hand, because imagination might someday find just such a joker in the
deck. My suspicion, however, is that there really are limits on what
reality can present us with. Intelligence and intention must be
built upon an edifice of complexity, along with the law of physics
and chemistry, any way we cut the cards. Five hundred years of
science, and five thousand of philosophy, have yet to sniff out any
alternatives, and seem unlikely ever to do so.

So
the supernatural is a non-starter, at least if we intend to stay true
to the themes of this book: curiosity, imagination, and the
scientific approach to explaining things. We have to find something,
or things, in what we already know, or can reasonably speculate
about, if life is to be laid out, dissected, elucidated in some
manner that satisfies us. What I experienced during my walk through
Pennypack Park begs for explanation as much as, if not more, than
anything else one might experience. But where does one begin this
journey towards enlightenment? How do we even start to think about
it?

* * *

Fortunately,
there is a place to start; not a place that makes everything that
follows easy or simple, but one that I believe at least parses the
subject of life into two separate, somewhat more manageable
sub-topics. One sub-topic is the question of the origin: how the
atoms and molecules that in early Earth were in arrangements almost
entirely non or pre-biological came to be re-assembled – or
super-assembled is perhaps the better term – into the most
primitive versions of our complexity plus (appearance of) purpose
life forms that appear first on this planet between three and a half
and four billion years ago.

Is
this a separate question? Yes, it clearly is, and for the following
reasons: first, all things biological, however large or small, or
ephemeral or long-loved, or whatever their form or function, or
however they eke out their livings, rely upon a common basis of
biochemistry which can be clearly seen in all of them, if you examine
them at the level of atoms and molecules. That in itself suggests a
common origin, and provides the platform for the other reason: this
platform, this origin aside, is what accounts for the overwhelming
diversity in livings things that we witness today, billions of years
after the beginnings, in the various shapes, colors, sizes, and
behaviors of the tens of millions of plants, animals, fungi, and
other species which have crawled, flown, walked, swam, or in whatever
manner reached practically every corner and niche of remotely
inhabitable space that can be found on Earth.

Here,
in the early twenty-first century, this cleavage of the problem of
life into these two daughter problems is supported by so much
evidence that there can be no doubt that it is the proper way to
initiate our quest. The chemical evidence from DNA, RNA, proteins,
carbohydrates, and other biomolecules has demonstrated their common
origin beyond any reasonable doubt. As an example, the viruses which
I have mentioned, so tiny that they cannot be seen by any optical
microscope however powerful, and whose relative simplicity makes
their place in the bower of biology still a disputed issue, can feast
upon hosts as disparate as bacteria and human beings and redwood
trees only because the molecular machinery underpinning all of these
things, including the viruses themselves, is almost identical. The
same could be said about the relationship between virulent bacteria
and their animal / plant / fungus hosts; for that matter, about the
plain, ordinary fact that most living things on this planet make
their living by somehow consuming other living things. This is
something that couldn’t happen if we weren’t all made up of the
same basic, chemical, stuff, underneath all our appearances of
diversity.

Of
course, it may still prove possible that the same kinds of processes
explain both phenomena, the origin of life, and its subsequent
diversification. But there is no reason to assume, a
priori,
that this is true, and in fact it is the position of almost all
scientists who tackle these two problems that it is almost certainly
not true, or at least not true for the most part though there may be
some overlap in some places.

What
is true, however, is that we are given a choice, right here and now,
at the start of our trek toward understanding. As in Robert Frost’s
poem, we are presented a choice of two roads to walk upon, both of
which seem equally enticing:

Two
roads diverged in a yellow wood,

And
sorry I could not travel both

And
be one traveler, long I stood

And
looked down one as far as I could

To
where it bent in the undergrowth;

Then
took the other, as just as fair,

And
having perhaps the better claim,

Because
it was grassy and wanted wear;

Though
as for that the passing there

Had
worn them really about the same,

And
both that morning equally lay

In
leaves no step had trodden black.

Oh,
I kept the first for another day!

Yet
knowing how way leads on to way,

I
doubted if I should ever come back.

I
shall be telling this with a sigh

Somewhere
ages and ages hence:

Two
roads diverged in a wood, and I—

I
took the one less traveled by

And
that has made all the difference.

Unlike
Frost’s poem, the two roads we are faced with look very unequal
even before we take the first step on either of them. Again,
beginning with our vantage point at the start of the twenty-first
century, we can say that one of these roads really is well-worn,
although there do remain many thickets and tangles and vines and
thorns to be waded through; while the other, superficially the more
straightforward of the two, is actually much more mired in
undergrowth and mystery, one on which many faltering first steps have
been made or attempted still with no clear path in sight. That
seemingly-clearer road is the problem of the origins of life; a
surprise only as long as we overlook the one, real, overwhelming
obstacle in our path: which is that, however it happened, it did so
either billions of years ago on this planet, or trillions of miles
away on other possible worlds as discussed in chapter two, and then
transported here; either of which leaves us exceedingly short of
useful data upon which we can build testable theories. Both of which
leave us prey to the purveyors of miracles, a shortage of which is
seemingly never found; as long as, however, we forget that if
miracles are answers, then science would never have explained
anything, and curiosity and imagination would be pointless. Even if
we do never solve some particular problem, this is no cause for
capitulation; we are, after all, mere human beings with human
abilities, and it shouldn’t surprise anyone that some questions
remain forever unanswered, no matter how much of those abilities are
applied to them for how long. It is quite possible that the origin
of life, or its different possible origins, remains a nut we never
quite crack. Disappointing as that would be, it is no cause for
dismay or futility or some kind of existential malaise; besides
which, we will no doubt discover many amazing things in our endeavors
to solve this problem. Indeed, this has already happened, with
examples of amazing self-organizing complexity in various chemical
systems being the most obvious examples. This is actually one of the
most amazing things about science, at least as I have experienced it:
that our attempts to hammer out a solution to one problem ends up
leading us completely unexpected paths, stumbling upon unknown veins
of gold.

* * *

The
problem of the origin(s) of life is a fascinating and of course
commanding one, one in which many books can and have been written on
and which careers have been dedicated to. However, I have
deliberately chosen to leave it out of this book because meandering
down so long a path with so many thickets and brambles is likely to
end up with ourselves just scratching ourselves all over, and mending
and binding the many wounds which we will receive, with no clear end
in sight as our reward. Actually, even Darwin himself knew this. In
all his tomes on evolution, he persistently avoids and evades the
question of life’s origins, leaving it in backwaters to be treaded
by the minds that were to come after him. If possible, he doesn’t
even mention or allude to it. He had the foresight and, in our
hindsight, the wisdom, to know that mucking around in those waters
would only muddy the tale he was bent on weaving, a tale with enough
problems of its own. Fittingly, it is a problem he only alights upon
to let us know that he too will have nothing of the supernatural in
solving it. Just as Newton was wise enough to know to let the cause
of the gravity he so deftly described be a problem left to his
successors, so Darwin also avoids this slippery trap and leaves the
question of origins to minds to come after him.

There
is one last point I would like to make here. It was well accepted by
the late eighteen hundreds that one of the most important
characteristics of livings things today is that all of them had
parents, of one form or another. That fact, so obvious to us now,
was finally nailed down by Louis Pasteur in a series of famous
experiments, thereby separating the problem of biology into its two
great sub-problems, its origins and its subsequent evolution. What
Pasteur showed was that wherever even the simplest of living things
came from, whether they be mice or maggots, they didn’t just burst
into existence out of inorganic or simple organic beginnings. No,
all of them, without exception, were begat in some manner; moms and
dads, or at least a parent of some sort, were involved, even if no
one knew in any detail how the begetting was done. You could breed
billions of bacteria from one bacterium, but not a one from zero,
however hard you tried. That clear and indisputable truth was a
beginning into everything the twentieth century contributed about the
fundamentals of biology: Everything comes from something, nothing
comes from nothing. At least not on this planet, at this point in
its history.

* * *

It
would appear that we at least have a beginning here in our wonderings
about ourselves, about life, that we can summarize. A quartet of
beginnings, actually. First is that it displays levels of
complexity, organization, and seeming purpose which would appear to
defy explanation. Second, at its most fundamental level, life and
its origins are based on nothing more than physics and chemistry,
most crucially on the amazing properties of that amazing element
carbon, although a plethora of other elements play essential roles as
well. In addition, we and our ancestors all share a common
biochemistry, a biochemistry built on DNA, proteins, and so forth,
and have certainly done so going back a good three billion plus years
in Earth’s history.

The
third beginning is an inevitable consequence of the first two, that
of procreation being the only way nature has now of producing new
organisms, from bacteria to human beings, that living things are
simply too complicated and organized to assemble by chance. Not only
that, but offspring resemble their parent(s) (although, of course
this is not always immediately obvious, as we all know from the
example of a caterpillar hatching from a butterfly’s egg), a
resemblance which will be passed on to future generations, albeit
with occasional mutations.

As
for the fourth beginning, evolution, that it occurs and has been
occurring for a vastly long time, that it explains the many forms and
functions and niches life has found on our world, and that, most
importantly, we possess the fundamental understanding of how and why
it occurs, underlays biology just as physics underlays chemistry and
mathematics underlays physics. Furthermore, just as our third
beginning derived from its predecessors, the fourth emerges
inevitably from the third. It is the beginning that took two English
naturalists, Charles Darwin and Alfred Russell Wallace, and these
Victorian gentlemen’s elegant and brilliant reasoning which derive
from the observation of two natural phenomena: the inheritance of
physical and behavioral traits from parent to offspring, and
competition for scarce resources among those offspring to survive and
repeat the process: natural selection. What to me makes their
accomplishments all the more remarkable is that how heredity works
was something neither man had a clear concept of (even though this
was the same time that Gregor Mendel was doing his experiments with
peas which would have helped both of them immensely – experiments
which remained in obscurity until the early 1900s); indeed, some of
Darwin’s concepts in this field actually made his theory harder to
defend. Still, they convinced the scientific establishment of their
day within a short period of time.

* * *

It
is natural selection and random mutation that have conspired together
over millions of years to wire our brains into the relentless
curious, pattern hunting, story weaving machines I spoke of in
chapter one. This unconscious conspiracy has been so successful that
we imagine that we see people and animals among the stars and, if
like most of us who have ever lived do not know better, believe tales
of how they came to be there. It is also of course one of the main
wellsprings of all art and literature, from the Mona Lisa and War and
Peace to the Campbell’s soup label and idle gossip. It is,
ironically, the reason that I used the word conspiracy and all it
implies without a second thought, and probably the reason you may not
have questioned my doing so.

The
obvious downside to this marvelous, compelling faculty of our brains
is that the patterns and stories are often unsuspicious products of
it. When this happens, then they, like magic, only sidetrack and
mislead us too, perhaps disastrously so. In fact, neither our brains
nor the rest of our bodies are the culmination of any kind of
conspiracy, but only one of many possible, logical outcomes of
nature’s blind laws.

So
we tread carefully when we look at the universe about and within us
and try to make sense of its workings and history. Each step has the
potential to take us either into deeper understanding or shallower
error. If we place too much trust in this part of what nature has
wired into us, we seriously risk the latter. We must always be
prepared to pull back to reexamine what we think we see, to be
skeptical, to consider other possibilities, and to use another gift
we have been given by those same blind laws, that of our ability to
reason. If we tread the path carefully enough, our prospects for
success, I believe, are promising.

Why
do I begin a discussion of evolution this way? The best answer I can
offer is to return to the beginning of this chapter: “One of
themes of this book is that if we are to satisfy our curiosity about
the universe around us, we will need to use our imaginations, because
the universe as we perceive it simply doesn’t get us very far.”

Yet
imagination stripped of pattern seeking and story telling would be a
moribund faculty of our minds, if indeed our minds could have it at
all. It surely would be nowhere close to the task of fleshing out
and filling in our understanding of things. Not that it would it
matter though for our curiosity would be almost severely crippled as
well, probably to no more than an animal instinct serving few goals
greater than finding food and mates and avoiding predators.

Nowhere
is this shown better than in the work on the structure and workings
of the DNA molecule, the beating heart of heredity, a heart that,
perhaps more than anything else science has discovered before or
since, would never have been found without that combination of
imagination, pattern seeking and story telling, skepticism, and
reason which make us such unique organisms that we may indeed be
alone (although I hope not) in the universe.

As
with so many other parts of my scientific education, I was first
exposed to DNA and its workings one of the Time-Life books (or maybe
it was one of Isaac Asimov’s many books on science). I was then
too young to understand it in much detail, but I do recall being
profoundly impressed with how important it was to all life on this
planet, and at least the rudiments of why. The deeper comprehension
was something that has taken a fair part of my life to even begin to
grasp, and even today I know that comprehension is nowhere near as
deep as it could be – not that I feel embarrassed or ashamed about
that for even the most brilliant minds in the world have spent both
this and a large part of the last century yet still have many
mysteries arrayed against them.

* * *

I
cannot resist a recapitulation here. It has been almost six months
since I took the stroll through Pennypack Park I described earlier in
this chapter, but right now, thinking of these issues, I find myself
irresistibly drawn back to that day. Doing so, I find that my senses
are as enthralled now as they were then. Once again I see and hear
and smell the many living things surrounding me, almost making me
feel as though I have been transported to some kind of paradise. For
here I am, surrounded by the oaks and the maples and the sycamores
and occasional pine trees, and admittedly many others I do not
recognize. The branches and twigs of bushes, both low and high,
brush against my body, and my shoes swish over the uncut grass.
Birds circle in the air, dart between the trees, then settle on their
branches and study the world around them. If I close my eyes, not
only do I hear their many languages, I am greeted by a cacophony of
other noises: insects of all kinds, the rustling of just opening
leaves in the spring breeze, the splashing of fish breaking the
surface of the still cold water, the dabbling and occasional quacking
of ducks, the distant, patient calls of bull frogs toward potential
mates, the scratching of squirrels racing up and down the trees, and
others which I cannot with any certainty place or, to be honest,
remember now. I am also of course aware of the humans around me and
their myriad tongues with their myriad emotions and hopes, not to
mention the clopping of those fortunate enough to be riding horses.
Dogs bark from time to time, also reminding me of our presence.
Opening my eyes again, I look for the other, more silent or better
concealed creatures I know to be about, from mice and ground hogs and
snakes, to ones like skunks, raccoons, opossums, and others that only
come out at night. I see no deer, but don’t doubt they are about,
that it is only a matter of time and attention. Stroking my fingers
on a stone wall I feel the velvet of new moss against my fingertips.
It is too early for mushrooms and most other fungi, but they too hide
in dark places, waiting for warmer weather and longer days to coax
them out. The insects I heard swirl around me now, and spiders lurk
in cracks in the stone walls or hang from fresh webs, waiting for
victims. Taking it all in, it is difficult to imagine how nature
could have been more creative in her choice of forms and functions
for her productions. Humans have nowhere near such power, and
perhaps never will.

Yet
I have only just brushed up against the most amazing thing about all
this splendor. Which is that, were we to take samples of all of it,
and place it under an instrument powerful enough to see that deeply
into the structure of life, they would all reveal the spirals of DNA
at the very core of their beings, spirals which account for that
amazing creativity. In no case would the spirals be exactly the same
– they would differ in their lengths and, in most places, their
specific nucleotide sequences – but the similarities would vastly
outweigh the differences in even the most distantly related
organisms. Walking through the park, we are inescapably aware of the
diversity which infinitely impresses us, yet it is only when we look
closer, much closer, do we see – probably the most profound paradox
of life on this world – the foundation which is shared by all of
it.

Which
is why of course I began by speaking of patterns and stories, and the
double-edged sword in our minds which compels us to see and create
them. If you will recall the beginning of this chapter, I dared the
reader to define what life actually is, and gave some examples of how
our forebears answered it. The important point about our forebears
is that the answers they did come up, as persuasive as they were to
them, could not have been more mistaken. The patterns they perceived
in life, and the stories they told to explain them and their origins,
however compelling and reasonable they seemed at the time, have
turned out to be wrong, dead wrong, in retrospect absurdly wrong.
What accounts for all living things is the laws of physics and
chemistry, working within the forces of evolution by natural
selection.

But
if we stop there we fail to appreciate the power of the other edge of
the sword. The discovery of DNA and the other molecules of heredity,
the probing into and teasing out how they work, would not have been
possible without our ability and willingness to use this edge as well
as all the other facets of imagination, in combination with the
hardest of scientific acumen. For what pattern in nature could be
more arresting than the DNA spiral? And what story could be more
captivating than the story that led to its discovery and unraveling –
except, perhaps, the story that DNA, and the millions of years it has
been evolving in so many directions, itself tells?

* * *

We
take it as common knowledge today that DNA (or, in some cases, its
brother molecule RNA) forms the hereditary basis for almost all
living things on this planet, but Darwin and Wallace died long before
it was discovered. Yet neither man could have failed to grasp the
power of this one molecule to fulfill its dual responsibilities as
the instruction set for both developing biological things and
maintaining so many of their essential functions. They would no
doubt have been equally impressed – no, elated – with its
additional ability to create new information via mutation,
information to be tested in the living, breathing, real world of life
and death. Natural selection could not have a greater ally.

I
have been emphasizing the almost incomprehensible complexity of
living things, but in describing DNA we are surprisingly impressed,
at least at first sight, by its simplicity. The simplicity is such
that Crick and Watson, who revealed its structure to the world a
little over fifty years ago (without, alas, giving Rosalind Franklin
her due credit), were able to deduce how it replicates itself –
something it must do every time a cell divides – without a single
additional observation or experiment to back their deduction up
(although they were rather cagey in how they mentioned it in their
paper). And although there are still much research to be done, we
have since that time been able to elucidate what DNA does and how it
does it with impressive detail.

Simplicity
does not mean lack of sophistication, however. DNA, comprised of two
strands of sugar phosphate backbones, twirled together and held that
way by pairs of small, interlocking “base pair” molecules, may
not sound promising as genetic material; it would probably not even
be the first choice of an engineer looking for an efficient molecule
for storing information. But remember the discussion earlier of the
power of the carbon atom to assemble stable molecules of very large
size. As large as, for example, the Hope diamond. The DNA contained
in chromosome one of the forty-six chromosomes of a single cell of
your body would, if teased out to its full length, be approximately
three inches long and contain over two hundred million base pairs (I
can’t resist the calculation that if all the DNA in all our cells
were laid end to end, they would stretch from here to the moon and
back some twelve thousand times!). Given that the four bases can
have any potential sequence, yielding 4200000000
or over 10100000000
possible arrangements in just that one chromosome, perhaps our
engineer should take a second look. Incidentally, don’t try: that
is a number no amount of imagination will make real in your mind;
even all the atoms in the entire known universe only sum up to less
than a paltry 1080.

Actually,
on third thought, if anything we seem to be dealing with such an
overkill of information storage capacity that we wonder why nature
chose to employ DNA at all. Would wonder, that is, if nature truly
were an intelligent engineer that could choose anything.

So
DNA, its deceptive initial simplicity aside, is easily – way easily
– more than up to the task of encoding all the information needed
to create and maintain not only ourselves, but also any living
organism we can conceive of, however strange and wondrous; more than
all the organisms that have ever lived on this planet, or might live
in the future. Or that might have or will live anywhere else in our
universe, assuming they use DNA as their genetic code. Or in a
billion billion universes (if they exist) spanning a billion billion
years.

Information
… but of what nature? And how is it encoded in the DNA spiral?
And how does our biological machinery and processes extract it, and
turn it into the raw material of our beings? And how has it allowed
the combination of random mutation and natural selection to drive
life from its simplest beginnings over three billion years ago to the
incredible diversity of much more complex forms, including ourselves,
that we see today – a diversity my walk through Pennypack Park only
revealed only the tiniest fraction of?

It
is time to talk about protein.

* * *

Here
is a subject we are all at least somewhat familiar with. Who doesn’t
remember as a child being cajoled, coaxed, and badgered into making
sure we ate enough protein to grow strong and tall? Go into any
health food store and you will find rows of large containers of
protein supplements, each promising to build stronger muscles in
absurdly short times.

Proteins
are large organic molecules (though nowhere near as large as DNA)
which, when we consume them, are broken down by digestive processes
into small molecular units called amino acids. There are some twenty
kinds of amino acids in living things, and different combinations and
numbers of them link together to make all the proteins nature
produces. Having broken down the proteins we eat, we then reassemble
the freed amino acids to construct the many new different proteins
our own bodies need. And our bodies need them for many different
purposes.

What
makes proteins so important and so versatile is the fact that they
are not merely random strings of amino acids, like glass beads on a
thread. Instead, because of the intramolecular forces in them, they
coil, wrap around each other, form plate-like structures, and then
fold up into specific, detailed shapes which are determined by their
specific sequences. That is why the glutinous, translucent “white”
of an egg becomes firm and truly white when we cook it, for heat, as
well as other physical and chemical assaults, unravels the globular
shape of the albumin proteins and make them lay flat against each
other.

The
myriad sizes and shapes of proteins are employed by bodies to perform
all kinds of functions. For example, proteins studding the surface
of a cell control the rate at which water and other molecules and
ions (electrically charged atoms and molecules) enter and leave.
They are employed in such diverse roles as construction material for
hair and nails and cartilage, and as essential components of
important biological molecules such as the hemoglobin in your blood,
which carries oxygen from your lungs to every cell in your body and
carries away the carbon dioxide waste to be exhaled. Numerous
different types are critical to cell metabolism, in particular those
that serve as enzymes, which catalyze chemical reactions in your
cells to produce other important molecules. The elasticity of
proteins in muscle cells allow those cells to expand and contract,
allowing your heart to beat and you to use your arms and legs. They
are also important in cell signaling and the proper functioning of
your immune system. Your parents were indeed wise to exhort you to
get enough of them in your diet, even if they did not know why.

Curiosity
ought to be provoking a question in your mind right about now.
Digestion breaks down the proteins we eat into their component amino
acids. The amino acids are then transported by the blood to all the
cells in the body. It is in our cells that all the proteins we
need are constructed. Yet proteins contain from hundreds to tens of
thousands of amino acids, all joined together in the specified orders
they require to perform their functions. The greatest engineer in
the world would be running out of his factory screaming if handed a
task this monumental. How do our cells handle it with such aplomb?

The
molecular machinery which assembles proteins in the cell is a subject
which, if I were an expert on it, I could easily fill the rest of
this chapter and more describing. Fortunately, I’m not an expert
on that particular topic, which means I can segue back to DNA without
further ado. The point in this discussion on proteins is that DNA is
the template which is used to build them. A gene is a section of DNA
serving as the template for a specific protein. More specifically,
the sequence of DNA bases determine the sequence of amino acids, the
correspondence between base and amino acid being three to one: each
amino acid corresponds to, is encoded by, three nucleotide bases in
succession. As there are four such bases, this gives us 4 × 4 × 4
= 64 possible amino acids we could code for, well more than the
twenty that are actually used in nature.

Actually,
this is worth elaborating on to some detail, due to another
digression I feel is worth making. If we represent the four
nucleotide bases in DNA, adenine, thymine, guanine, and cytosine, by
their initial letters, A, T, G, and C, we find that we have an
excellent “quaternary” coding system to work with. I use the
word quaternary here in the same way the word “binary” is used
when discussing computer code. When you run your favorite computer
program, or even much less than favorite program, the code your
computer is executing is essentially nothing more than a series of
(electronic) 0s and 1s. This series of 0s and 1s tell the computer’s
processing chip(s) and all the associated electronics and other
gizmos what to do (some of which you saw in chapter two); bear in
mind that with enough 0s and 1s we can create a computer program as
sophisticated as we like; if my understanding of computer science is
correct, given enough 0s and 1s we could create a program that
simulated the entire universe and its history, though whether this
universe includes the program and the computer it is running on is
still unclear to me.

The
three to one correspondence between bases and amino acids modifies
the coding system of DNA but does not alter the analogy with computer
programming code, an analogy I would like to continue with. It means
that if we were to read the amino acid sequence of a section of DNA
by “unzipping” it and looking at the base sequence, instead of
looking at it one base at a time we would have to read it in groups
of three: e. g., TTA, CAG, CTG, GCA, and so on, each group of three
coding for one acid. As noted, that is well more than enough for the
twenty amino acids nature uses in living things.

Computer
programming. Like one of the individuals who have inspired this
book, I too have had considerable experience in the field and so too
am drawn to the comparison of DNA to programming code. It is a
powerful and compelling comparison – the idea of DNA as digital
information, to be molded in any direction the blind but non-random
forces of evolution wield – has, for me at least, as much appeal to
imagination and useful insight as any other idea in biology over the
last quarter century or so. Now, with the digital age fully upon us,
the comparison, or analogy, is even more forceful to the mind.
Personally, as a (very) part-time science fiction writer it conjures
up images of artificial living beings, of synthetic organs and
tissues to prolong our lives, perhaps indefinitely, of expanding the
already impressive capacities of our brains with biochips, and even
such cybernetic ideas as an Internet composed of human minds directly
connected to and communicating with each other and with sentient
computers. Given that I honestly expect to see some of this happen
at least in my lifetime not to mention my children’s, the digital
view of biology is perhaps too
seductive.

* * *

After
everything I have said about imagination and our need to use it to
answer our questions about ourselves and our universe, the word
seductive alone ought to suggest I am about to pull back, at least
somewhat. So I am. Not that I don’t truly believe that many if
not all of the above mentioned wonders of coming technology will
happen someday. But the emphasis on the digital nature of DNA can
potentially mislead us as well as inform.

The
reason for this is that our digital DNA codes, serves as a template
for, the highly analog proteins that are the actual machinery of our
bodies. By analog I simply mean the opposite of digital: continuous
in change as opposed to changing in discrete steps. (A hopefully not
too outdated example of the difference would be the analog dial on
old radio sets which, as you turned it, changed the tuning of the
receiver continuously from one frequency to another, as opposed to
digital push-button radios today which jump instantly to a specific
frequency.) In calling proteins analog, I do not mean the sequence
of amino acids which comprise them; that is still as digital as DNA
in that an amino acid change in the sequence is discrete – you
can’t continuously change between one acid and another.

Hang
on, for I am getting to the reason for this digression. It is true
that the amino acid sequence in a protein is digital, but what
matters for proteins, what they do and how they work, is largely
their specific size and shape, qualities that usually can be varied
more or less continuously by changes in the amino acid sequence which
comprises them. That is, if we replace one amino acid in a protein
consisting of hundreds or thousands with another, the most likely
outcome is a small, perhaps even insignificant, change in its shape –
resulting in a proportionately tiny change in how the protein does
its job. For example, if the protein is an enzyme, a slight change
in its shape would cause the rate at which it catalyzes its specific
reaction to be somewhat faster or slower. Or if the protein controls
the rate at which a certain molecule or ion enters or leaves cells,
that could be modified slightly. Furthermore, additional amino acid
changes are likely to lead to similar small, cumulative changes in
the protein’s function.

Small,
cumulative changes. We are practically talking about the heart and
soul of Darwinian evolution. But what would cause these single amino
acid changes in a protein’s make-up? Recall that it is a
particular sequence of three consecutive nucleotide bases on DNA
which correspond to the amino acid at a particular location in a
protein. Any number of agents have the potential to alter, or
“mutate” a base in DNA: radiation and various kinds of chemical
assaults. Such mutations (there are others) even has a name: point
mutations. Point mutations are surprisingly common. Most are caught
and corrected by molecular machinery in the cell designed for the
purpose, but they occasionally slip through the defenses. In doing
so they can lead to the amino acid changes in proteins which often
(not always: sickle-cell anemia is caused by just such a single
change on one of the globin proteins in hemoglobin) cause those
proteins’ functioning to alter slightly, causing somewhat higher or
lower production of another chemical or modifying cell membrane
permeability to a molecule / ion, leading to … well, for example,
if the protein is involved in embryological development, a modest
change in the physiology or behavior of the organism. The point is,
when talking about natural selection, modest changes, such as those
that lead to slightly longer or shorter legs, have a better chance of
being advantageous than large changes, which are almost certain to be
disastrous. And given that changes can accumulate over geological
time, constantly being molded and “directed” by natural
selection, I hope it is by now clear that the entire edifice of DNA /
proteins / form and function, though completely unknown in Darwin’s
and Wallace’s time, could hardly have been better tailored to the
revolutionary ideas they unleashed upon the world.

* * *

Wondering
about ourselves is, of course, an endeavor that never ends, and no
such pretense will be made here. On the contrary, the territory
covered in this chapter is only a tiny fraction of the vast subject
of life, what it is and how it has come to be. Alas, curiosity
demands more, far more much more, than I could hope to deliver even
in an entire book, assuming I was well versed enough in the subject
for such an undertaking. But I do hope that certain basics about
life, in general, have been laid down: its utterly improbable
complexity, seeming design and purposefulness (what I have called
intentionality); the underlying chemistry, particularly of carbon,
that makes it possible (on our planet); the continuity, in that all
living organisms are in some way descended from a parent or parents,
going back to the beginnings of life on Earth some three and a half
or more billion years ago; the basics of Darwinian / Wallician
evolution, which explains how life today came from its much simpler
beginnings; and the interworkings of the tapestry of DNA with the
working machinery of proteins which are essential to both life’s
functioning and its evolution. I hope you feel that we have not made
a bad start.

But
there is another aspect to our self exploration, one that can’t be,
and won’t be, ignored. That is our wondering about ourselves as
individuals. How is it, each of us asks at least from time to time,
that I
came to be; what and why am I; what is my place and destiny, if any,
in the scheme of things, whatever that scheme is assuming; what does
it mean to be human and what else could I have been? The reason I
have excluded this aspect from this chapter is that the sciences that
answer it, if any, are necessarily more speculative, to the point
where it is questionable in many cases to call them sciences at all.
But that doesn’t stop our asking the questions. It doesn’t
quench our curiosity, or make it go away. And we can still use our
imaginations – gingerly, for we tread on unknown territories – in
our quest to come up with answers that just might make some degree of
sense. Or so we hope.

About Me

My formal training is in chemistry. I also read a great deal of physics and biology. In fact I very much enjoy reading in general, mostly science, but also some fiction and history. I also enjoy computer programming and writing. I like hiking and exploring nature. I also enjoy people; not too much in social settings, but one on one; also, people with interesting or "off-beat" minds draw me to them. I also have some interest in Buddhism.

These days I get a lot more information from the internet, primarily through Wiki. Some television, e. g., documentaries, PBS shows like "Nova" and "Nature".

My favorite science writers are Jacob Bronowski ("The Ascent of Man") and Richard Dawkins (his "The Blind Watchmaker" is right up there up Ascent). I also have a favorite writer on Buddhism, Pema Chodron. Favorite films are "Annie Hall" (by Woody Allen), "The Maltese Falcon", "One Flew Over The Cuckoo's Nest", "As Good As It Gets", "Conspiracy Theory", Monty Python's "Search For The Holy Grail" and "Life of Brian", and a few others which I can't think about at the moment.

I love a number of classical works (Beethoven's "Pastoral", "Afternoon Of A Fawn" and "Clair De Lune" by Debussey , Pachelbel's "Canon" come to mind. My favorite piece is probably Gershwin's "Rhapsody in Blue". But I also enjoy a great deal in modern music, including many jazz pieces, folk songs by people like Dylan, Simon and Garfunkel, a hodgepodge of pieces by Crosby, Stills, and Nash, Niel Young, and practically everything the Beatles wrote.

My life over the last few years has been in some disarray, but I am finally "getting it together.". As I am very much into the sciences and writing, I would like to move more in this direction. I also enjoy teaching. As for my political leanings, most people would probably describe as basically liberal, though not extremely so. My religious leanings are to the absolutely none: I've alluded to my interest in Buddhism, but again this is not any supernatural or scientifically untested aspect of it but in the way it provides a powerful philosophy and set of practical, day to day methods of dealing with myself and the other human beings.